FMO DATABASE

FMODB ID: 4Y5YN

Calculation Name: 3RK2-A-Xray547

Preferred Name: Synaptosomal nerve-associated protein 25 (SNAP-25)

Target Type: SINGLE PROTEIN

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RK2

Chain ID: A

ChEMBL ID: CHEMBL2364159

UniProt ID: P60880

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	30
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-103432.561629
FMO2-HF: Nuclear repulsion	90863.151113
FMO2-HF: Total energy	-12569.410516
FMO2-MP2: Total energy	-12605.780802

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:31:ARG)

Summations of interaction energy for fragment #1(A:31:ARG)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-42.926	-39.936	0.008	-1.177	-1.821	-0.005

Interaction energy analysis for fragmet #1(A:31:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.834 / q_NPA : 1.895

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	33	GLN	0	0.076	0.027	3.605	3.187	5.365	-0.010	-0.956	-1.212	-0.004
4	A	34	GLN	0	-0.014	0.008	3.399	10.053	10.865	0.018	-0.221	-0.609	-0.001
5	A	35	THR	0	0.012	0.008	4.819	3.015	3.015	0.000	0.000	0.000	0.000
6	A	36	GLN	0	-0.063	-0.039	6.808	4.142	4.142	0.000	0.000	0.000	0.000
7	A	37	ALA	0	0.041	0.017	8.513	4.293	4.293	0.000	0.000	0.000	0.000
8	A	38	GLN	0	-0.001	0.001	8.338	0.492	0.492	0.000	0.000	0.000	0.000
9	A	39	VAL	0	-0.021	-0.007	10.750	3.340	3.340	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.844	-0.915	12.767	-37.770	-37.770	0.000	0.000	0.000	0.000
11	A	41	GLU	-1	-0.940	-0.964	13.757	-37.165	-37.165	0.000	0.000	0.000	0.000
12	A	42	VAL	0	-0.006	-0.013	14.648	2.518	2.518	0.000	0.000	0.000	0.000
13	A	43	VAL	0	-0.017	-0.006	16.704	2.280	2.280	0.000	0.000	0.000	0.000
14	A	44	ASP	-1	-0.849	-0.917	18.424	-27.595	-27.595	0.000	0.000	0.000	0.000
15	A	45	ILE	0	-0.049	-0.024	17.871	1.785	1.785	0.000	0.000	0.000	0.000
16	A	46	MET	0	-0.019	-0.020	20.719	1.584	1.584	0.000	0.000	0.000	0.000
17	A	47	ARG	1	0.874	0.941	20.992	28.874	28.874	0.000	0.000	0.000	0.000
18	A	48	VAL	0	0.056	0.029	24.338	1.096	1.096	0.000	0.000	0.000	0.000
19	A	49	ASN	0	-0.058	-0.040	24.183	1.427	1.427	0.000	0.000	0.000	0.000
20	A	50	VAL	0	0.002	0.003	26.613	0.795	0.795	0.000	0.000	0.000	0.000
21	A	51	ASP	-1	-0.882	-0.933	28.685	-20.132	-20.132	0.000	0.000	0.000	0.000
22	A	52	LYS	1	0.934	0.966	27.530	22.347	22.347	0.000	0.000	0.000	0.000
23	A	53	VAL	0	-0.055	-0.030	30.483	0.627	0.627	0.000	0.000	0.000	0.000
24	A	54	LEU	0	0.020	0.015	32.351	0.584	0.584	0.000	0.000	0.000	0.000
25	A	55	GLU	-1	-0.936	-0.971	34.579	-17.161	-17.161	0.000	0.000	0.000	0.000
26	A	56	ARG	1	0.861	0.919	34.875	17.973	17.973	0.000	0.000	0.000	0.000
27	A	57	ASP	-1	-0.951	-0.967	36.833	-16.005	-16.005	0.000	0.000	0.000	0.000
28	A	58	GLN	0	-0.012	-0.017	38.619	0.215	0.215	0.000	0.000	0.000	0.000
29	A	59	LYS	1	0.814	0.915	38.141	16.282	16.282	0.000	0.000	0.000	0.000
30	A	60	LEU	-1	-0.965	-0.951	39.637	-14.007	-14.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:ARG)